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The first genomic landscape of Chilean gallbladder cancer, in 56 tumours, found TP53, TSC2 and NOTCH1 the most mutated genes, actionable changes in ATM, BRCA1/2, EGFR and ERBB2, and a hint that Mapuche ancestry goes with TP53 mutation.
118 tumour samples were collected, of which 56 passed sequencing quality control on the Oncomine Comprehensive Assay v1. Somatic variants were annotated with ANNOVAR and the Cancer Genome Interpreter, ancestry was inferred with ADMIXTURE and principal components on ancestry-informative markers, and comparisons were made with Japanese, Singaporean and United States cohorts.
535 somatic mutations were detected in 43 genes, with TP53 (30%), TSC2 (29%) and NOTCH1 (27%) most frequently mutated. 121 clinically actionable variants were identified in ATM, BRCA1/2, EGFR, ERBB2 and other genes. Exploratory analysis suggested an association between higher Mapuche ancestry and TP53 mutations, and comparative analyses revealed distinct mutational patterns in the Chilean cohort relative to Asian and United States datasets.
Chile has the world's highest gallbladder cancer mortality and until this paper almost no tumour genomics; the lower TP53 rate and high TSC2 and NOTCH1 hint at a different mutational grammar, but the panel and sample size mean the figures need replication.
Shares BRCA1 / BRCA2 (HRD), HER2, Gallbladder cancer.
Shares BRCA1 / BRCA2 (HRD), TP53, HER2, Gallbladder cancer.
Shares BRCA1 / BRCA2 (HRD), TP53.
Shares ATM, BRCA1 / BRCA2 (HRD).
Shares BRCA1 / BRCA2 (HRD), TP53.
Shares ATM, BRCA1 / BRCA2 (HRD), TP53.
Shares ATM, BRCA1 / BRCA2 (HRD), TP53.
Shares BRCA1 / BRCA2 (HRD), TP53.